bio-alignment 0.0.7 → 0.0.8

data/README.md

@@ -19,6 +19,8 @@ Features are:
 * Support for BioRuby trees and node distance calculation
 * bio-alignment interacts well with BioRuby structures,
   including sequence objects and alignment/tree parsers
+* Support for textual and HTML output of MSA (planned)
+* Support for Clayton's MAF parser is (planned)
 
 When possible, BioRuby functionality is merged in. For example, by
 supporting Bio::Sequence objects, standard BioRuby alignment
@@ -34,7 +36,39 @@ Bio::BioAlignment
 document](https://github.com/pjotrp/bioruby-alignment/blob/master/doc/bio-alignment-design.md)
 for Ruby.
 
-## Developers
+## Command line
+
+bio-alignment comes with a command line interface (CLI), which can apply a number
+of editing functions on an alignment, and generate textual and HTML
+output. Note that the CLI does not cover the full library. The CLI can be useful
+for non-Rubyists, pipeline setups, and simply as examples
+
+Remove bridges (columns with mostly gaps) from an alignment
+
+    bio-alignment aa-alignment.fa --type aminoacid --edit bridges
+
+Mask islands (short misaligned 'floating' parts in a sequence) 
+
+    coming soon...
+
+Mask serial mutations
+
+    coming soon...
+
+Remove all sequences consisting of mostly gaps (30% informative) and output to FASTA
+ 
+    bio-alignment codon-alignment.fa --type codon --edit info --out fasta
+
+or output codon style
+
+    bio-alignment codon-alignment.fa --type codon --edit info --style codon
+
+Remove all sequences containing gaps from an alignment (why would you
+want to do that?)
+
+    bio-alignment codon-alignment.fa --type codon --edit info --perc 100 --out fasta
+
+## Section for developers
 
 ### Codon alignment example
 
@@ -50,7 +84,7 @@ aligmment (note codon gaps are represented by '---')
   aln = Alignment.new
   fasta = FastaReader.new('codon-alignment.fa')
   fasta.each do | rec |
-    aln.sequences << CodonSequence.new(rec.id, rec.seq)
+    aln << CodonSequence.new(rec.id, rec.seq)
   end
   # write a matching amino acid alignment
   fasta = FastaWriter.new('aa-aln.fa')
@@ -106,18 +140,35 @@ BioAlignment supports adding BioRuby's Bio::Sequence objects:
   include Bio::BioAlignment
 
   aln = Alignment.new
-  aln.sequences << Bio::Sequence::NA.new("atgcatgcaaaa")
-  aln.sequences << Bio::Sequence::NA.new("atg---tcaaaa")
+  aln << Bio::Sequence::NA.new("atgcatgcaaaa")
+  aln << Bio::Sequence::NA.new("atg---tcaaaa")
+```
+
+or use BioRuby's flat file reader
+
+```ruby
+  aln = Alignment.new
+  Bio::FlatFile.auto(filename).each_entry do |entry|
+    aln << entry
+  end
 ```
 
-and we can transform BioAlignment into BioRuby's Bio::Alignment and
-use BioRuby functions
+and, the other way, we can transform BioAlignment into BioRuby's
+Bio::Alignment and use BioRuby functions
 
 ```ruby
   bioruby_aln = aln.to_bioruby_alignment
   bioruby_aln.consensus_iupac
 ```
 
+Note that native BioRuby objects may not always work. In the first
+case, using Bio::Sequence::NA, no ID is passed in, so each sequence is
+labeled 'id?'. In the second case BioRuby's FlatFile returns a
+FastaFormat object, this time with ID, but FastaFormat does not
+support indexing. In general, it is recommended to stay with the
+bio-alignment Sequence classes (or roll your own, as long as they are
+Enumerable). 
+
 ### Pal2nal
 
 A protein (amino acid) to nucleotide alignment would first load
@@ -132,7 +183,7 @@ the sequences
   aln2 = Alignment.new
   fasta2 = FastaReader.new('nt.fa')
   fasta2.each do | rec |
-    aln2.sequences << Sequence.new(rec.id, rec.seq)
+    aln2 << Sequence.new(rec.id, rec.seq)
   end
 ```
 
@@ -174,15 +225,17 @@ BioAlignment has support for attaching a phylogenetic tree to an
 alignment, and traversing the tree using an intuitive interface
 
 ```ruby
-  sole_tree = Bio::Newick.new(string).tree  # use BioRuby's tree parser
-  tree = aln.attach_tree(sole_tree)         # attach the tree
-  # now do stuff with the tree, which has improved bio-align support
+  newick_tree = Bio::Newick.new(string).tree  # use BioRuby's tree parser
+  tree = aln.attach_tree(newick_tree)         # attach the tree
+  # now do stuff with the tree, which has improved bio-alignment support
   root = tree.root 
   children = root.children
   children.map { |n| n.name }.sort.should == ["","seq7"]
   seq7 = children.last
   seq4 = tree.find("seq4")
   seq4.distance(seq7).should == 19.387756600000003 
+  # find the sequence in the alignment belonging to the node
+  print seq4.sequence
   print tree.output_newick                  # BioRuby Newick output
 ```
 
@@ -201,13 +254,14 @@ programming. Primitives are provided which take out much of the
 plumbing, such as maintaining row/column/element state, and allow
 copy-on-edit (so no conflicts arise in concurrent code). For example,
 to walk an alignment by row, and update the row state, you can mark
-all rows for deletion which contain many gaps
+all rows (sequences) which contain many gaps for deletion
 
 ```ruby
   include MarkRows
   mark_rows { |rowstate,row|  # for every row/sequence
     num = row.count { |e| e.gap? }
     if (num.to_f/row.length) > 0.5
+      # this row in the alignment consists mostly of gaps
       rowstate.delete!  # mark row for deletion
     end
     rowstate   # returns the updated row state
@@ -225,9 +279,9 @@ The general idea is that there are many potential ways of selecting
 rows, and changing some state. The 'mark_rows' function/iterator takes
 care of the plumbing. All the programmer needs to do is to set the
 criterion, in this case a gap percentage, and tell the library what
-state has to change. In this example we only access one row, but you
-can also access the other rows. You won't be surprised that marking
-columns looks much the same
+state has to change. In this example we only access one row at a time,
+but you can also access the other rows. You won't be surprised that
+marking columns looks much the same
 
 ```ruby
   include MarkColumns
@@ -262,7 +316,7 @@ and, here we remove every marked element by turning it into a gap
 the old with the new. 
 
 It is important to note that, instead of directly editing alignments
-in place, this module always makes it a two step process. First items
+in place, bio-alignment always makes it a two step process. First items
 are masked/marked through the state of the rows/columns/elements, next
 the alignment is rewritten using this state. The advantage of using an
 intermediate state is that the state can be queried for creating (for
@@ -286,6 +340,9 @@ An edit feature is added at runtime(!) Example:
 
 where aln2 is a copy of aln with bridging columns deleted.
 
+More examples can be found in the features/edit directory of the
+source.
+
 ### See also
 
 For more on the design of bio-alignment, read the

data/TODO

@@ -0,0 +1,2 @@
+- Island masking assumes one unique element, maybe consider a
+  neighbour. The example in test/data is rather a good one.

data/VERSION

@@ -1 +1 @@
-0.0.7
+0.0.8

data/bin/bio-alignment

@@ -1,12 +1,22 @@
 #!/usr/bin/env ruby
 #
 # BioRuby bio-alignment Plugin
-# Version 0.0.0 
 # Author:: Pjotr Prins
 # Copyright:: 2012
 # License:: The Ruby License
 
- USAGE = "Describe bio-alignment"
+rootpath = File.dirname(File.dirname(__FILE__))
+$: << File.join(rootpath,'lib')
+
+_VERSION = File.new(File.join(rootpath,'VERSION')).read.chomp
+
+$stderr.print "bio-alignment "+_VERSION+" Copyright (C) 2012 Pjotr Prins <pjotr.prins@thebird.nl>\n\n"
+
+USAGE =<<EOU
+
+bio-alignment transforms alignments
+
+EOU
 
 if ARGV.size == 0
   print USAGE
@@ -14,51 +24,63 @@ end
 
 require 'bio-alignment'
 require 'optparse'
+include Bio::BioAlignment
 
-# Uncomment when using the bio-logger 
-# require 'bio-logger'
-# Bio::Log::CLI.logger('stderr')
-# Bio::Log::CLI.trace('info')
+log = Bio::Log::LoggerPlus.new 'bio-alignment'
 
-options = {:example_switch=>false,:show_help=>false}
+Bio::Log::CLI.logger('stderr')
+Bio::Log::CLI.trace('info')
+
+options = {show_help: false}
+options[:show_help] = true if ARGV.size == 0
 opts = OptionParser.new do |o|
-  o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
+  o.banner = "Usage: #{File.basename($0)} [options] filename\n\n"
 
-  o.on('--example_parameter [EXAMPLE_PARAMETER]', 'TODO: put a description for the PARAMETER') do |example_parameter|
-    # TODO: your logic here, below an example
-    options[:example_parameter] = 'this is a parameter'
+  o.on('--type codon|nucleotide|aminoacid', [:codon,:nucleotide,:aminoacid], 'Type of sequence data (default auto)') do |type|
+    options[:type] = type.to_sym
   end
-  
-  o.separator ""
-  o.on("--switch-example", 'TODO: put a description for the SWITCH') do
-    # TODO: your logic here, below an example
-    self[:example_switch] = true
+
+  o.on('--edit bridges|islands|info', [:bridges,:islands,:info], 'Apply edit function') do |edit|
+    options[:edit] = edit.to_sym
   end
 
-  # Uncomment the following when using the bio-logger 
-  # o.separator ""
-  # o.on("--logger filename",String,"Log to file (default stderr)") do | name |
-  #   Bio::Log::CLI.logger(name)
-  # end
-  #
-  # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
-  #   Bio::Log::CLI.trace(s)
-  # end
-  # 
-  # o.on("-q", "--quiet", "Run quietly") do |q|
-  #   Bio::Log::CLI.trace('error')
-  # end
-  # 
-  # o.on("-v", "--verbose", "Run verbosely") do |v|
-  #   Bio::Log::CLI.trace('info')
-  # end
-  # 
-  # o.on("--debug", "Show debug messages") do |v|
-  #   Bio::Log::CLI.trace('debug')
-  # end
+  o.on('--perc value', Integer, 'Percentage') do |v|
+    options[:perc] = v
+  end
+
+  o.on('--out fasta', [:fasta], 'Output format') do |format|
+    options[:out] = format.to_sym
+  end
+
+  o.on('--style codon', [:codon], 'Output style') do |style|
+    options[:style] = style.to_sym
+  end
+
+  o.separator ""
+
+  o.on("--logger filename",String,"Log to file (default stderr)") do | name |
+    Bio::Log::CLI.logger(name)
+  end
+  
+  o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
+    Bio::Log::CLI.trace(s)
+  end
+  
+  o.on("-q", "--quiet", "Run quietly") do |q|
+    Bio::Log::CLI.trace('error')
+  end
+  
+  o.on("-v", "--verbose", "Run verbosely") do |v|
+    Bio::Log::CLI.trace('info')
+  end
+  
+  o.on("--debug", "Show debug messages") do |v|
+    Bio::Log::CLI.trace('debug')
+  end
 
   o.separator ""
-  o.on_tail('-h', '--help', 'display this help and exit') do
+
+  o.on_tail('-h', '--help', 'Display this help and exit') do
     options[:show_help] = true
   end
 end
@@ -66,11 +88,67 @@ end
 begin
   opts.parse!(ARGV)
 
-  # Uncomment the following when using the bio-logger 
-  # Bio::Log::CLI.configure('bio-alignment')
+  if options[:show_help] 
+    print opts
+    print USAGE
+  end
 
-  # TODO: your code here
-  # use options for your logic
 rescue OptionParser::InvalidOption => e
   options[:invalid_argument] = e.message
 end
+
+Bio::Log::CLI.configure('bio-alignment')
+logger = Bio::Log::LoggerPlus['bio-alignment']
+logger.info [options, ARGV]
+
+ARGV.each do |fn|
+  aln = Alignment.new
+  Bio::FlatFile.auto(fn).each_entry do |entry|
+    case options[:type]
+      when :codon
+        aln << CodonSequence.new(entry.entry_id,entry.seq)
+      when :nucleotide 
+        aln << Sequence.new(entry.entry_id,entry.seq)
+      when :aminoacid
+        aln << Sequence.new(entry.entry_id,entry.seq)
+      else
+        # auto uses BioRuby sequence type
+        logger.warn "Using native type, if you encounter a problem, set the --type explicitly"
+        aln << entry
+    end
+  end
+  case options[:edit]
+    when :bridges
+      logger.info "Apply delete bridges"
+      require 'bio-alignment/edit/del_bridges'
+      aln.extend(DelBridges)
+      aln2 = aln.del_bridges
+      aln = aln2
+    when :islands
+      logger.info "Apply mask islands filter"
+      require 'bio-alignment/edit/mask_islands'
+      aln.extend(MaskIslands)
+      marked_aln = aln.mark_islands
+      aln2 = marked_aln.update_each_element { |e| (e.state.masked? ? Element.new("X"):e)}
+      aln = aln2
+    when :info
+      logger.info "Apply sequence information filter"
+      require 'bio-alignment/edit/del_non_informative_sequences'
+      aln.extend(DelNonInformativeSequences)
+      aln.each { |seq| seq.extend(State) }
+      aln2 = aln.del_non_informative_sequences(options[:perc])
+      aln = aln2
+    else 
+      # do nothing
+  end
+  case options[:out]
+    when :fasta
+      aln.each do | seq |
+        print FastaOutput::to_fasta(seq)
+      end
+    else
+      aln.each do | seq |
+        print TextOutput::to_text(seq,options[:style])
+      end
+  end
+end

data/features/phylogeny/tree-feature.rb

@@ -78,6 +78,11 @@ Then /^find that "([^"]*)" is on the same branch as "([^"]*)"$/ do |arg1, arg2|
   seq.nearest.map{|n|n.to_s}.sort.join(',').should == arg2
 end
 
+Then /^find that the alignment sequence matching tree node "(.*?)" is "(.*?)"$/ do |arg1, arg2|
+  tree = @aln.attach_tree(@tree)
+  node = tree.find(arg1)
+  node.sequence.to_s.should == arg2
+end
 
 Then /^draw the MSA with the tree$/ do | string |
   # textual drawing, like tabtree, or http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-talk/149701

data/features/phylogeny/tree.feature

@@ -28,6 +28,7 @@ Feature: Tree support for alignments
     And find that the nearest sequence to "seq1" is "seq2,seq3"
     And find that "seq1" is on the same branch as "seq2,seq3"
     And find that "seq4" is on the same branch as "seq1,seq2,seq3,seq5,seq8"
+    And find that the alignment sequence matching tree node "seq4" is "----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV"
     And draw the MSA with the tree
       """
       ,--9.69----------------------------------------- seq7  ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM

data/features/support/env.rb

@@ -0,0 +1,19 @@
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
+require 'bio-alignment'
+
+require 'rspec/expectations'
+
+log = Bio::Log::LoggerPlus.new 'bio-alignment'
+
+Bio::Log::CLI.logger('stderr')
+Bio::Log::CLI.trace('info')
+

data/lib/bio-alignment.rb

@@ -2,9 +2,14 @@
 # bioruby directory tree.
 #
 
+require 'bio-logger'
+require 'bio-alignment/coerce'
 require 'bio-alignment/state'
 require 'bio-alignment/elements'
 require 'bio-alignment/sequence'
 require 'bio-alignment/codonsequence'
 require 'bio-alignment/tree'
 require 'bio-alignment/alignment'
+require 'bio-alignment/format/text'
+require 'bio-alignment/format/fasta'
+require 'bio-alignment/format/phylip'

data/lib/bio-alignment/alignment.rb

@@ -13,6 +13,7 @@ module Bio
       include Pal2Nal
       include Rows
       include Columns
+      include Coerce
 
       attr_accessor :sequences
       attr_reader :tree
@@ -44,7 +45,7 @@ module Bio
 
       # return an array of sequence ids
       def ids
-        rows.map { |r| r.id }
+        rows.map { |r| Coerce::fetch_id(r) }
       end
 
       def size
@@ -56,6 +57,10 @@ module Bio
         rows[index]
       end
 
+      def << seq
+        @sequences << seq
+      end
+
       def each
         rows.each { | seq | yield seq }
         self
@@ -68,21 +73,23 @@ module Bio
 
       def find name
         each do | seq |
-          return seq if seq.id == name
+          return seq if Coerce::fetch_id(seq) == name
         end
         raise "ERROR: Sequence not found by its name, looking for <#{name}>"
       end
      
-      # clopy alignment and allow updating elements
+      # copy alignment and allow updating elements. Returns alignment.
       def update_each_element
         aln = self.clone
         aln.each { |seq| seq.each_with_index { |e,i| seq.seq[i] = yield e }}
+        aln
       end
 
       def to_s
         res = ""
         res += "\t" + columns_to_s + "\n" if @columns
-        res += map{ |seq| seq.id.to_s + "\t" + seq.to_s }.join("\n")
+        # fetch each sequence in turn
+        res += map{ |seq| Coerce::fetch_id(seq).to_s + "\t" + Coerce::fetch_seq_string(seq) }.join("\n")
         res
       end
 
@@ -106,7 +113,7 @@ module Bio
       # the tree traverser
       def attach_tree tree
         extend Tree
-        @tree = Tree::init(tree)
+        @tree = Tree::init(tree,self)
         @tree
       end
 
@@ -122,6 +129,7 @@ module Bio
         new_aln.attach_tree(new_tree.clone)
         new_aln
       end
+
     end
   end
 end

data/lib/bio-alignment/bioruby.rb

@@ -4,7 +4,7 @@ module Bio
     class NA
       include Enumerable
       def each
-        to_s.each_byte do | c |
+        to_s.each_char do | c | 
           yield c
         end
       end
@@ -12,7 +12,7 @@ module Bio
     class AA
       include Enumerable
       def each
-        to_s.each_byte do | c |
+        to_s.each_char do | c |
           yield c
         end
       end

data/lib/bio-alignment/codonsequence.rb

@@ -7,13 +7,16 @@ module Bio
     # Codon element for the matrix, used by CodonSequence.
     class Codon
       GAP = '---'
-      UNDEFINED = 'X'
+      UNDEFINED = 'XXX'
 
       attr_reader :codon_table
+      include State
 
       def initialize codon, codon_table = 1
         @codon = codon
         @codon_table = codon_table
+        @codon.freeze
+        @codon_table.freeze
       end
 
       def gap?
@@ -32,6 +35,10 @@ module Bio
         @codon
       end
 
+      def == other
+        @codon == other.to_s
+      end
+
       # lazily convert to Amino acid (once only)
       def to_aa
         aa = translate
@@ -52,7 +59,7 @@ module Bio
       # lazy translation of codon to amino acid
       def translate
         @aa ||= Bio::CodonTable[@codon_table][@codon]
-        @aa
+        @aa.freeze
       end
     end
 
@@ -72,6 +79,9 @@ module Bio
         seq.scan(/\S\S\S/).each do | codon |
           @seq << Codon.new(codon, @codon_table)
         end
+        @id.freeze
+        @codon_table.freeze
+        # @seq is not immutable, as we can add new codes to the list
       end
 
       def [] index
@@ -86,6 +96,7 @@ module Bio
         @seq.each { | codon | yield codon }
       end
 
+      # Output codon style
       def to_s
         @seq.map { |codon| codon.to_s }.join(' ')
       end
@@ -107,7 +118,11 @@ module Bio
       def << codon
         @seq << codon
       end
-        
+
+      # Return Sequence (string) as an Elements object
+      def to_elements
+        self
+      end
     end
 
   end

data/lib/bio-alignment/coerce.rb

@@ -0,0 +1,45 @@
+module Bio
+  module BioAlignment
+    module Coerce
+      # Make BioRuby's entry_id compatible with id
+      def Coerce::fetch_id seq
+        if seq.respond_to?(:id)
+          seq.id
+        elsif seq.respond_to?(:entry_id)
+          seq.entry_id
+        else
+          "id?"
+        end
+      end
+
+      # Coerce BioRuby's sequence objects to return the sequence itself
+      def Coerce::fetch_seq seq
+        if seq.respond_to?(:seq)
+          seq.seq
+        else
+          seq
+        end
+      end
+
+      # Coerce sequence objects into a string
+      def Coerce::fetch_seq_string seq
+        s = fetch_seq(seq)
+        if s.respond_to?(:join)
+          s.join
+        else
+          s.to_s
+        end
+      end
+
+      # Coerce sequence objects into elements
+      def Coerce::to_elements seq
+        if seq.respond_to?(:to_elements)
+          seq.to_elements
+        else
+          Elements.new(fetch_id(seq),fetch_seq(seq))
+        end
+      end
+    end
+  end
+end
+

data/lib/bio-alignment/columns.rb

@@ -37,7 +37,7 @@ module Bio
       end
 
       def columns_to_s
-        columns.map { |c| (c.state ? c.state.to_s : '?') }.join
+        columns.map { |c| (c.respond_to?(:state) ? c.state.to_s : '?') }.join
       end
        
       def clone_columns!
@@ -50,21 +50,31 @@ module Bio
       end
     end
 
-    # Support the notion of columns in an alignment. A column
-    # can have state by attaching state objects
+    # Support the notion of columns in an alignment. A column is simply an
+    # integer index into the alignment, stored in @col. A column can have state
+    # by attaching state objects.
     class Column
       include State
       include Enumerable
 
       def initialize aln, col
         @aln = aln
-        @col = col
+        @col = col # column index number
+        @col.freeze
+        @aln
       end
 
       def [] index
         @aln[index][@col] 
       end
 
+      # update all elements in the column
+      # def update! new_column
+      #   each_with_index do |e,i|
+      #     @aln[i][@col] = new_column[i]
+      #   end
+      # end
+
       # iterator fetches a column on demand, yielding column elements
       def each
         @aln.each do | seq |

data/lib/bio-alignment/edit/del_non_informative_sequences.rb

@@ -5,11 +5,15 @@ module Bio
 
     module DelNonInformativeSequences
       include MarkRows
-   
+  
+      # Count the informative elements in a sequence. If the count
+      # is less than +percentage+ mark the sequence for deletion.
+      #
       # Return a new alignment with rows marked for deletion, i.e. mark rows
       # that mostly contain undefined elements and gaps (threshold
       # +percentage+). The alignment returned is a cloned copy
       def mark_non_informative_sequences percentage = 30
+        percentage=30 if not percentage # for CLI
         mark_rows { |state,row| 
           num = row.count { |e| e.gap? or e.undefined? }
           if (num.to_f/row.length) > 1.0-percentage/100.0
@@ -20,7 +24,7 @@ module Bio
       end
 
       def del_non_informative_sequences percentage=30
-        mark_non_informative_sequences.rows_where { |row| !row.state.deleted? }
+        mark_non_informative_sequences(percentage).rows_where { |row| !row.state.deleted? }
       end
     end
   end

data/lib/bio-alignment/edit/edit_rows.rb

@@ -5,7 +5,7 @@ module Bio
     # state, and returning a newly cloned alignment
     module MarkRows
 
-      # Mark each seq
+      # Mark each seq and return alignment
       def mark_rows &block
         aln = markrows_clone
         aln.rows.each do | row |
@@ -16,11 +16,15 @@ module Bio
 
       # allow the marking of elements in a copied alignment, making sure 
       # each element is a proper Element object that can contain state.
+      #
       # A Sequence alignment will be turned into an Elements alignment.
+      #
+      # Returns the new alignment
       def mark_row_elements &block
         aln = markrows_clone
         aln.rows.each_with_index do | row,rownum |
-          new_seq = block.call(row.to_elements,rownum)
+          new_seq = block.call(Coerce::to_elements(row),rownum)
+          # p [rownum,new_seq,row]
           aln.rows[rownum] = new_seq
         end
         aln
@@ -32,13 +36,15 @@ module Bio
         aln = self.clone 
         # clone row state, or add a state object 
         aln.rows.each do | row |
-          new_state =
-            if row.state
-              row.state.clone
-            else
-              RowState.new
-            end
-          row.state = new_state
+          if row.respond_to?(:state)
+            new_state =
+              if row.state
+                row.state.clone
+              else
+                RowState.new
+              end
+            row.state = new_state
+          end
         end
         aln
       end

data/lib/bio-alignment/edit/mask_islands.rb

@@ -13,25 +13,33 @@ module Bio
         end
       end
 
-      # Drop all 'islands' in a sequence with low consensus, that show a gap
-      # larger than 'min_gap_size' (default 3) on both sides, and are shorter
-      # than 'max_island_size' (default 30). An island larger than 30 elements
-      # is arguably no longer an island, and low consensus stretches may be
-      # loops - it is up to the alignment procedure to get that right. We also
-      # allow for micro deletions inside an alignment (1 or 2 elements).
-      # The island consensus is calculated by column. If more than 50% of the
-      # island shows consensus, the island is retained. Consensus for each
-      # element is defined as the number of matches in the column (default 1).
+      # Drop all 'islands' in a sequence with low consensus, i.e. islands that
+      # show a gap larger than 'min_gap_size' (default 3) on both sides, and
+      # are shorter than 'max_island_size' (default 30). An island larger than
+      # 30 elements is arguably no longer an island, and low consensus
+      # stretches may be loops - it is up to the alignment procedure to get
+      # that right. We also allow for micro deletions inside an alignment (1 or
+      # 2 elements).  The island consensus is calculated by column. If more
+      # than 50% of the island shows consensus, the island is retained.
+      # Consensus for each element is defined as the number of matches in the
+      # column (default 1).
       def mark_islands
-        mark_row_elements { |row,rownum|
-          # first set state and find unique elements (i.e. consensus)
+        logger = Bio::Log::LoggerPlus['bio-alignment']
+        count_marked_islands = 0
+        count_marked_elements = 0
+
+        # Traverse each row in the alignment
+        marked_aln = mark_row_elements { |row,rownum|
+          # for each element create a state object, and find unique elements (i.e. consensus) across a column
           row.each_with_index do |e,colnum|
             e.state = IslandElementState.new
             column = columns[colnum]
             e.state.unique = (column.count{|e2| !e2.gap? and e2 == e } == 1)
             # p [e,e.state,e.state.unique]
           end
-          # group elements into islands (split on gap) and mask
+          # at this stage all elements of the row have been set to unique,
+          # which are unique. Now group elements into islands (split on gap)
+          # and mask
           gap = []
           island = []
           in_island = true
@@ -52,7 +60,9 @@ module Bio
                 gap << e
                 if gap.length > 2
                   in_island = false
-                  mark_island(island)
+                  ci, ce = mark_island(island)
+                  count_marked_islands += ci
+                  count_marked_elements += ce
                   # print_island(island)
                   island = []
                 end
@@ -60,41 +70,29 @@ module Bio
             end
           end
           if in_island
-            mark_island(island)
+            ci, ce = mark_island(island)
+            count_marked_islands += ci
+            count_marked_elements += ce
             # print_island(island) if island.length > 0
           end
-          # row.each_with_index do |e,colnum|
-          #   e.state = ElementState.new
-          #   column = columns[colnum]
-          #   e.state.mask! if column.count{|e2| !e2.gap? and e2 == e } == 1
-          #   # print e,',',e.state,';'
-          # end
-          # now make sure there are at least 5 in a row, otherwise
-          # start unmasking. First group all elements
-          # group = []
-          # row.each_with_index do |e,colnum|
-          #   next if e.gap?
-          #   if e.state.masked?
-          #     group << e
-          #   else
-          #     if group.length <= min_serial
-          #       # the group is too small
-          #       group.each do | e2 |
-          #         e2.state.unmask!
-          #       end
-          #     end
-          #     group = []
-          #   end
-          # end
-          row  # return changed sequence
+          row # always return the row to mark_row_elements
         }
+        logger.info("#{count_marked_islands} islands marked (#{count_marked_elements} elements)")
+        return marked_aln
       end
 
     private
-
+    
+      # Check a list of elements that form an island. First count the number
+      # of elements marked as being unique. If the island is more than 50%
+      # unique (i.e. less than 50% consensus with the rest if the alignment) 
+      # all island elements are marked for masking. Returns the number of
+      # islands and elements marked as a tuple
       def mark_island island
-        return if island.length < 2
+        return 0,0 if island.length < 2
         unique = 0
+        count_islands = 0
+        count_elements = 0
         island.each do |e|
           unique += 1 if e.state.unique == true
         end
@@ -104,7 +102,10 @@ module Bio
           island.each do |e|
             e.state.mask!
           end
+          count_islands += 1
+          count_elements += island.size
         end
+        return count_islands, count_elements
       end
 
       def print_island island

data/lib/bio-alignment/elements.rb

@@ -10,6 +10,7 @@ module Bio
 
       def initialize c
         @c = c
+        @c.freeze
       end
       def gap?
         @c == GAP
@@ -23,6 +24,13 @@ module Bio
       def == other
         to_s == other.to_s
       end
+      def clone
+        e = self.dup
+        if e.state != nil
+          e.state = e.state.clone
+        end
+        e
+      end
     end
 
     # Elements is a container for Element sequences. 
@@ -34,6 +42,7 @@ module Bio
       attr_reader :id, :seq
       def initialize id, seq
         @id = id
+        @id.freeze
         @seq = []
         if seq.kind_of?(Elements)
           @seq = seq.clone
@@ -75,7 +84,7 @@ module Bio
       def clone
         copy = Elements.new(@id,"")
         @seq.each do |e|
-          copy << e.dup
+          copy << e.clone
         end
         copy
       end

data/lib/bio-alignment/format/fasta.rb

@@ -0,0 +1,17 @@
+module Bio
+  module BioAlignment
+    module FastaOutput
+      def FastaOutput::to_fasta seq
+        buf = ">"
+        buf += seq.id+"\n"
+        buf += if seq.kind_of?(CodonSequence) 
+                 seq.to_nt
+               else
+                 seq.to_s
+               end
+        buf+"\n"
+      end
+    end
+  end
+end
+

data/lib/bio-alignment/format/phylip.rb

@@ -0,0 +1,25 @@
+module Bio
+  module BioAlignment
+    module PhylipOutput
+      # Calculate header info from alignment and return as string
+      def PhylipOutput::header alignment
+        "#{alignment.size} #{alignment[0].length}\n"
+      end
+
+      # Output sequence PAML style and return as a multi-line string
+      def PhylipOutput::to_paml seq, size=60
+        buf = seq.id+"\n"
+        coding = if seq.kind_of?(CodonSequence) 
+                 seq.to_nt
+               else
+                 seq.to_s
+               end
+        coding.scan(/.{1,#{size}}/).each do | section |
+          buf += section + "\n"
+        end
+        buf
+      end
+    end
+  end
+end
+

data/lib/bio-alignment/format/text.rb

@@ -0,0 +1,18 @@
+module Bio
+  module BioAlignment
+    module TextOutput
+      
+      def TextOutput::to_text seq, style
+        res = ""
+        res += Coerce::fetch_id(seq).to_s + "\t"
+        res += if seq.kind_of?(CodonSequence) and style == :codon
+                 seq.to_s
+               else
+                 Coerce::fetch_seq_string(seq)
+               end
+        res+"\n"
+      end
+
+    end
+  end
+end

data/lib/bio-alignment/rows.rb

@@ -28,6 +28,7 @@ module Bio
       def initialize aln, row
         @aln = aln
         @row = row
+        freeze
       end
 
       def count &block

data/lib/bio-alignment/sequence.rb

@@ -11,6 +11,7 @@ module Bio
       attr_reader :id, :seq
       def initialize id, seq
         @id = id
+        @id.freeze
         @seq = seq
       end
 
@@ -18,6 +19,10 @@ module Bio
         @seq[index]
       end
 
+      # def []= index, value  --- we should not implement this for reasons of purity
+      #   @seq[index] = value
+      # end
+
       def length
         @seq.length
       end

data/lib/bio-alignment/tree.rb

@@ -11,13 +11,13 @@ module Bio
       class Node
       end
 
-      # Make all nodes in the Bio::Tree aware of the tree object so we can use
-      # its methods
-      def Tree::init tree
+      # Make all nodes in the Bio::Tree aware of the tree object, and the alignment, so
+      # get a more intuitive API
+      def Tree::init tree, alignment
         if tree.kind_of?(Bio::Tree)
           # walk all nodes and infect the tree info
           tree.each_node do | node |
-            node.inject_tree(tree)
+            node.inject_tree(tree, alignment)
           end
           # tree.root.set_tree(tree)
         else
@@ -38,8 +38,10 @@ module Bio
   class Tree
     class Node
       # Add tree information to this node, so it can be queried 
-      def inject_tree tree
+      def inject_tree tree, alignment
         @tree = tree
+        @tree.freeze
+        @alignment = alignment
         self
       end
 
@@ -102,6 +104,15 @@ module Bio
         end
         cs
       end
+
+      # Return the alignment attached to the tree
+      def alignment
+        @alignment
+      end
+
+      def sequence
+        @alignment.find(name)
+      end
     end  # End of injecting Node functionality
 
     def find name

data/spec/bio-alignment_spec.rb

@@ -108,3 +108,18 @@ describe "BioAlignment::DelBridges for codons" do
   aln3 = aln2.columns_where { |col| !col.state.deleted? }
   aln3.columns.size.should == 399
 end
+
+# require 'bio'  # BioRuby
+require 'bio-alignment/bioruby' # make Bio::Sequence enumerable
+
+describe "BioAlignment::BioRuby interface" do
+  include Bio::BioAlignment
+
+  aln = Alignment.new
+  aln << Bio::Sequence::NA.new("atgcatgcaaaa")
+  aln << Bio::Sequence::NA.new("atg---tcaaaa")
+  aln[0].should == "atgcatgcaaaa"
+  aln[1].should == "atg---tcaaaa"
+  Coerce::fetch_seq_string(aln[0]).should == "atgcatgcaaaa"
+  test = Coerce::fetch_id(aln[0])  # JRuby may have a name collision with object.id
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-alignment
 version: !ruby/object:Gem::Version
-  version: 0.0.7
+  version: 0.0.8
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-25 00:00:00.000000000Z
+date: 2014-05-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &83191660 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *83191660
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &83191360 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +37,15 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *83191360
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &83190960 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +53,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *83190960
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bio-bigbio
-  requirement: &83190640 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -54,10 +69,15 @@ dependencies:
         version: 0.1.3
   type: :development
   prerelease: false
-  version_requirements: *83190640
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: 0.1.3
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &83190190 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +85,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *83190190
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &83095350 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +101,15 @@ dependencies:
         version: 2.10.0
   type: :development
   prerelease: false
-  version_requirements: *83095350
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.10.0
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &83094950 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +117,15 @@ dependencies:
         version: 1.0.21
   type: :development
   prerelease: false
-  version_requirements: *83094950
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &83094400 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,7 +133,12 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *83094400
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Alignment handler for multiple sequence alignments (MSA)
 email: pjotr.public01@thebird.nl
 executables:
@@ -107,6 +147,7 @@ extensions: []
 extra_rdoc_files:
 - LICENSE.txt
 - README.md
+- TODO
 files:
 - .document
 - .rspec
@@ -115,6 +156,7 @@ files:
 - LICENSE.txt
 - README.md
 - Rakefile
+- TODO
 - VERSION
 - bin/bio-alignment
 - doc/bio-alignment-design.md
@@ -144,10 +186,12 @@ files:
 - features/phylogeny/tree.feature
 - features/rows-feature.rb
 - features/rows.feature
+- features/support/env.rb
 - lib/bio-alignment.rb
 - lib/bio-alignment/alignment.rb
 - lib/bio-alignment/bioruby.rb
 - lib/bio-alignment/codonsequence.rb
+- lib/bio-alignment/coerce.rb
 - lib/bio-alignment/columns.rb
 - lib/bio-alignment/edit/del_bridges.rb
 - lib/bio-alignment/edit/del_non_informative_sequences.rb
@@ -158,6 +202,9 @@ files:
 - lib/bio-alignment/edit/mask_serial_mutations.rb
 - lib/bio-alignment/edit/tree_splitter.rb
 - lib/bio-alignment/elements.rb
+- lib/bio-alignment/format/fasta.rb
+- lib/bio-alignment/format/phylip.rb
+- lib/bio-alignment/format/text.rb
 - lib/bio-alignment/pal2nal.rb
 - lib/bio-alignment/rows.rb
 - lib/bio-alignment/sequence.rb
@@ -186,7 +233,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 900281341
+      hash: 3021753307968946034
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -195,7 +242,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.6
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: Support for multiple sequence alignments (MSA)